I think some things are designed for a reason. I believe the cover actually forces air across components, cooling them before exhausting. (and duh, keeping crap from falling into the computer and shorting things out).
I had a 69 VW bug once (actually 6) and took off all of the aluminum that surrounded the motor so it would look cool and (I thought) it would run cooler. It overheated almost immediately. The aluminum I removed, forces air around the motor cooling it via an internal fan. Of course this has nothing to do with a computer, but I had to share my "removing stuff" overheat story.